Sonic:The Brotherhood of Shadows
by SonicWizard
Summary: (Sequel to War for Mobius)
1. Chapter 1

Sonic: The Brotherhood of Shadows

A sequel to The War for Mobius

If you haven't read that story, then go read that one first.

You all caught up? Then let's a-go!

Chapter One: Handling with Death

It's been a few months since Sonic's sacrifice to kill Unicron. Since then, more heroes have been popping up. (Slight OC Alert)

Inferno, a brash Hedgehog who grew up listening to old stories about a blue hedgehog's war with the evil dictator they hide from. He wields flames like Blaze does.

Vanix the Elephant was a knight of Acorn, the sovereign kingdom that took over, and polluted it's strong morality and legacy. Vanix wishes to undo Eggman's destruction, all without powers, besides his immense Elephant strength.

Aniyah the Squirrel took a more 'vigilante' approach. She goes by the code name of "Ambush" and uses her skills she acquired from an old teacher, who just so happened to have trained Espio.

Uru the Fox is Ambush's partner. He goes by the name of 'Blackout', because his powers are electricity related. He was a good friend with a little Tails.

Those few, along with others, have taken center stage against 's maniacal empire.

The old guard, Tails, Knuckles, the like? Mentors to the new heroes, who go to them for advice.

"Tails? When are we going to attack Eggman?" Flyby asked, bored. She chose to stay behind, without the other Transformers.

"As soon as I finish with your new weapons; a chaos energy powered sword and shield, which can be stored in your new arm gauntlets I installed into your forearms the other day." Tails replied.

Flyby looked stunned. "Wow, you really thought this through..."

Just then, a giant explosion rocked the new Tails Labs, which is now stationed in Station Square, the haven and fortress which houses the city, humans, Mobians, and the new heroes.

Inferno busted through the door. "Eggman is here!"

Tails swiftly turned his head. "What?! Here, Flyby, I'm going to install this in you real quick, then we bust some robotic chops!"

He connected it to the Gauntlets.

Flyby transformed into the newly minted X-Tornado and flew off, Tails in cockpit.

Station Square was literally on fire.

Vanix and some G.U.N soldiers were defending the house district, while Blackout and Ambush were defending the factory district. Inferno and Knuckles were defending the center of the city, while everyone else were shooting cannons, missiles, and even lasers at the oncoming attackers.

"Tails, Shadow's trying to patch to comms. Should I answer?" Flyby asked.

"Yes, Flyby, you may," He answered.

"Tails, we are dying out here, suspected casualties: 43,000 soldiers. 1,382 civillains. We can't let either of those numbers rise. Take out the mothership, then we can deal with the bombers," Shadow said.

"Wow, Shadow, you are really militaristic now. Taken your new job to heart?" Flyby asked.

"The commander is sick, someone had to take over."

Meanwhile...

A cloaked figure whispered to his fellow cloaked.

"This war threatens to reveal us. If the world knows we exist, then our power over this world..."

Another one speaks. "...all gone."

The one, dressed in a more fancy cloak, and with an amulet around his neck, rose from his throne. "We will not interfere directly. Instead, we move our pawns, and let them alter the course of events."

All nodded in agreement.

One cloaked person said, "If only our greatest Knight of Shadows was still alive."

The amulet cloaked person nodded. "If only Sonic were alive, he would fix this mess. He kept the evil doctor at bay. Perhaps we can bring our legendary knight back to life."

A cloaked figure rose. "No! Sonic, that blasted knight did nothing for us! All he was...he was a pawn! Like the others we control. Now, if we had recruited Shad-"

He was interrupted by the obvious leader, the fancier cloaked person. He walked over to him.

"Ah, yes. Shadow... hehe, Shadow. That is our goal, for Shadow to join us. But yet, he remains, out of reach. Alias, Shadow is a delicate object. But very special. He would be no pawn. He would be a Knight...no, a Grand Knight. Truly one of us. But, if we mess up even slightly our chances of receiving him would be quite dire. So if you wish to rush that slow, yet necessary path...hehe, it would be very...deadly..."

He picked up a encrusted dagger with a shiny ruby in the shape of a Chaos Emerald.

"You and I, we are not connected like the others...so I have no regret..."

He struck with the dagger.

"...in killing you."

The ruby glowed, and the figure's eyes shined, he then collapsed off the blade, and died.

A lesser cloaked figure grabbed him, and took him out of the meeting hall.

"And with that, our Knight's resurrection shall commence."


	2. Chapter 2

Chapter Two: Resurrection

"As with all beings who join the Brotherhood of Shadows, we store their blood in vials, the same blood required to be taken at join. As for our Knights, they are stored with the altar of Resurrection. Now, every once and awhile, the Altar will mess up and the resurrected shall die immediately, and we lose their blood, forever washed away, like tears in rain." The amulet cloaked one told the others as they walked towards the alter.

He grabbed the vial, the Knight's name inscribed.

He pored it into the altar, and with a black emerald in the center of the ancient battery, the blood swirled, and went down it's drain.

The emerald let out tons of jolts of black and purple lightning, striking the altar.

The Amulet glowed, and the figure wearing it walked into the lightning's line of fire, and it struck him, like a lightning rod.

"7 infinities bonded by dark and light, with we which command, beings born of the impurity, let us command once more, our force bonded to which powers the Altar, which powers the stars, which powers us. Let the circle be complete...ILLUMINUS!" He said, the purple lightning encapsulating the room in a swirling circle.

The lightning went down the well, and a figure arose from the well. Cast in liquid peach color, a being arose. The knight had reawakened.

The being with the amulet walked towards the figure, dripping wet with the liquid.

"Is your connection to the 7 infinities still intact?"

"Yes."

"Is it unpure?"

"Tainted beyond comprehension."

"Will you still command the impurity?"

"Yes, I will control the impurity."

"The bond is still intact with us? The inpurity? The 7 infinites? Are you even intact with yourself? Or has this whole ritual failed, and brought us a pawn, not a Knight?"

"It is...intact. I am still myself, and whatsoever not a pawn."

"It's good to have you back then, Knight. Station Square is under attack, and so are your...friends. Also, new heroes have popped up to take your place. One of them is another knight, so you will be with true friends. Now go, impress the world with your return, Knight. Make the Brotherhood proud."


	3. Chapter 3

Chapter Three: The Return of Sonic The Hedgehog

Sonic raced through the forest, arriving to the city.

He repositioned Egg-Pawn guns at one another at super speeds, making them destroy themselves.

He went over to Shadow, currently in one place because of Sonic's slowed down perspective. He put a paper in his hand, which was tickets to the new "Linken Forest" Concert.

Sonic dashed to Tails, and smashed a Egg-Pawn into the ground...in front of Tails's eyes.

He winked, then dashed off.

Tails collapsed then and there

The massive siege was practically over, ships colliding into one another. The enemy forces were decimated in less than a second.

The battle for Station Square was over.

"No, no, no NO!" Eggman shouted as he shot missiles at Sonic, but he caught and hurled it back at him, exploding and damaging the mothership.

Eggman reeled back. "No. You're dead. You are DEAD! I know you are dead!"

Sonic busted through the control window, and strutted over to Eggman.

"Sure I'm real. Let me show you!" He said as he snapped his fingers. The robots on the room were either cut in half and exploded, or smashed into the wall at extreme speeds.

"Please, don't kill me, g-ghost..."

"I won't. I have morals, you know. But what I will do? Crash this mothership."

Eggman's eyes filled with tears. Sonic destroyed the engines and watched it crash and burn. It landed and started to crush itself under its weight.

Sonic ran down it as explosions and hull instabilities happened all over the place. He dodged the gun fire, and kicked away the random Egg-Pawn.

He saw Eggman's hover pod leave, so he knew he was alive, much to the Brotherhood's dismay.

Sonic jumped off the hull just as he got to the crushing exploding part and landed quite smoothly, and the civilians shouted happily and the new heroes practically cheered.

Sonic was back. He was here to stay.


	4. Chapter 4

By **this point, I have the story written. Now what I'm going to do is to release chapters daily, to build tension!**

Chapter Four: The Brotherhood's Rage

"He left him alive, all-master," A cloaked Brotherhood member told the Amulet Cloaked person.

"Hmm. Investigate further."

The cloaked shook his head. "You don't get it. He's always been a hard knight to keep a knight. But now...the impurity doesn't want him anymore. He's too much a force for good. And the latest thing he did? That severely tipped his scales."

The All-Master yelled. "Bring him to me!"

Militaristic soldiers busted into Tails's Lab.

Sonic woke up, and kicked one back out the window, knocking him on the scaffolding.

Sonic shoved another's head through his desk, and kicked another one against the wall. Hoping to get attention.

Luckily, he woke up Knuckles.

He busted through the door, and saw some soldiers rapping up his hand and gagging him. One even had a syringe.

Knuckles howled in anger and preceded to "One Punch" everything.

He took off the gag. "You ok?" He asked.

"Yeah...I'm fine. I think I know what to do now. Thanks for the help, Knux."

"Anytime, Sonic!"

He walked out the room, and Sonic leapt out the window, diving downwards, air rushing past his fur, ears, and eyes. He caught himself on a nearby building and threw himself to another.

Just then, Ambush knocked Sonic down and he rolled against the handlebars on the roof.

"You work for the Brotherhood, don't you?!" She yelled.

Sonic got up. "What are you talking about?"

She glared. "I know. I know you do. I'm going to beat some answers out of you!"

He smirked. "Why don't you try, Aniyah?"

Her eyes widened. "How did you...?"

"You'd actually fit in well there, Aniyah. You already have the skills."

She kicked at Sonic, but he blocked and swung himself over her and threw her.

She stumbled on the ground, but got up. "Traitor! Don't you know what the Brotherhood's true goal is?"

"Create stable order and peace throughout Mobius, and then other worlds!"

She laughed. "No, it is to conquer EVERYTHING and strip us of our freedom!"

He turned back. "You know a lot. Are you that one person that they told me about? Who also works for the Brotherhood?"

She stepped back, shocked. "L...Liar!"

She threw a punch, but he ducked and spin jumped upwards, practically upper cutting her and she slammed hard against the ground. She did a spinning kick, and it knocked Sonic back, but he quickly regained balance and speed kicked her into the ground, cracking the floor.

He landed on the floor. " I need to investigate."


	5. Chapter 5

Chapter Five: Secrets

He arrived at the brotherhood's base. He opened the door. He saw some Brotherhood soldiers.

Sonic quickly grabbed both of their heads and slammed their heads together.

He quickly searched the vault of secrets. It was a room filled with reports and files.

He opened one of the boxes labeled "Sonic".

What he found was nauseating.

Doctor's reports, X-Rays, his mission reports, even his birth certificate... Everything was here.

Stuff even before he joined.

Meanwhile...

"We have reason to believe the Vault of Secrets has been opened by a non-authorized person."

The All-Master's fist clenched. "Slit their throats."

Back at the vault...

Sonic searched the box labeled "Top Secret". It was filled with war plans... Tons of them!

Sonic glared and pulled out a file labeled "Tactical Timeline."

He opened it and saw a whole bunch of pictures and reports. But these were sorted by date, not personnel, like the others. He then heard footsteps.

He threw himself onto a shady corner just as the soldiers arrived. They had live rounds and searched the place.

Sonic quickly dashed out the door, before any soldiers could notice and went back to Tails's Lab.

He ran up the building and sat in bed.

He checked the file, and he managed to keep all the papers in the file.

He saw an entire conspiracy unfold in front of his eyes.

"Assignments...Sonic...move the war in favor of the Brotherhood...4/14/91..."

"The Brotherhood dates back 78 years... First assignment...Project:Tentacle."

He continued reading.

"Project:Tentacle was a way to entangle the Brotherhood in even everyday lives. Oh Chaos, what've I worked for?" He said, on the verge of crying.

He looked up and saw Ambush waiting there.

"What's that? Your next hit?"

Sonic shook his head. "It's everything. All the way back 78 years. To the beginning."

She grabbed the file and rifled through it. "My Gaia!" She shouted.

Sonic got up and covered her mouth. "Quiet! If any civilians hear you, the Brotherhood'll know! I saw in there, they have 7 agents stationed in every important building!"

She nodded, understanding.

"Now, I wasn't kidding earlier. They have one hero on their side. Be careful on who you talk to."

She nodded once more, and Sonic lifted his hand.

Knuckles came bursting through the door, obviously drunk.

"Hey, my dudes, just wunderin' what's up..?"

Sonic glared at Knuckles. "Go home, Knuckles, you're drunk."

His breath was incalculably bad. "Sure thing, Shadow, have fun with Amy! Heheh..." He said as he closed the door.

"Yeesh."

She shook her head. "He's been like that since you died."

He turned around. "Really?"

"Yeah, now I wonder if he can even quit...now that you're back."

"I don't think anyone could," Sonic said in agreement.


	6. Chapter 6

Chapter Six: Thriller

The next day...

Sonic was with Inferno.

"Hey, I need you, Inferno. You mind helping me?"

Inferno looked at Sonic. "I'd love too!"

Sonic smirked. "Then come with me!"

He took him to the Brotherhood's base.

"I'm gonna need you to torch some stuff."

Inferno nodded, smiled, and created a fire ball in his hand.

Sonic opened the door, and had him throw it at the vault of secrets after he took the base's schematics and the top secret box.

"Alright, let's go!" Sonic shouted as both of them rocketed at sub-sonic speeds.

The All-Master watched the vault burn as he fell to his knees yelling.

"Sir, Sonic has slipped away from the impurity. He is now pure."

The All-Master looked behind him. He screamed in rage. "Sonic did this. I know. We now hunt him down...and I will kill him. With my dagger."

He pulled out the same dagger, still blood-soaked.

Sonic went back to his room, and Inferno left, yet still full of questions.

Tails came into the room. "'Hey, Sonic? What's that? And what did you do with Inferno?"

Sonic gave him the Tactical Timeline folder.

"What's this?" He asked.

"Don't tell anyone. Don't speak about it. There are 7 members in this facility willing to kill you for that. One of these new heroes is a member."

Tails now was puzzled and slightly scared.

"What members? What are they members of?!"

Both of them heard clanking.

"GO!" He shouted, and Tails ran with the file.

Sonic checked around, to make sure there wasn't a file he didn't hide.

He saw the soldiers blow up his wall, and then, chaos ensured.


	7. Chapter 7

Chapter Seven: Darkness Falls

Tousaan sat by the pond in Darkness Falls. She sat by her brothers.

She thought about Sonic. She didn't know about Unicron's arrival, or that he died during the fight against Unicron. All she thought about that day was that it was very windy. Remember, Darkness Falls' forest was so plentiful that it blocked out the Sun, and it blocked their view of the World-Eater.

Just then, soldiers busted through the trees and such, shooting at everything.

They killed many of her brothers, resembling assassins.

"Please, stop!" She yelled.

One of the soldiers hit her against the wall.

And the All-Master came into view.

"You will tell us where your son, Sonic the Hedgehog is."

"My son?" Tousaan asked.

"Don't play coy. We know about you and his father...you are the genetical mother."

Tousaan snarled, then screamed at him. "What do you want with my boy?!"

The All-Master smirked. "To kill him."

She snarled, howled, and stabbed into a soldier's side, breaking out of his hold.

The All-Master's amulet glowed bright pink and purple and black lightning zapped her backwards. "You will tell me...NOW!"

She screamed in pain. "I don't know!" was all she could muster.

The All-Master's lightning stopped. "Thank you for your time."

She tried to get up, but she couldn't. She started to cry, scared for her son.


	8. Chapter 8

Chapter Eight: G.U.N Overthrown

Shadow was on the floor, bleeding. Gunfire scorched the air. Shadow got up and shot a G.U.N Soldier.

He sat right back down.

Another G.U.N Soldier shot his machine gun, covering Shadow. "Run! Now!" Shadow ordered as he threw a Chaos spear, exploding the entrance, covering them.

A Soldier kicked open a door, and threw a grenade at a nearby group of G.U.N Soldiers. They shot at Shadow before they exploded.

They leapt off a balcony, and then they saw a G.U.N dropship.

It dropped walkers and transforming small planes.

A Soldier threw a grenade at a Walker, exploding it to pieces. Shadow homing attacked the rest, and threw a Chaos Spear at the DropShip, exploding it.

A soldier in Shadow's group stabbed Shadow. "Acckk!" He said as he fell over. He pulled out the knife and threw it into the soldier's stomach. He then kicked it, shoving it through the soldier.

Shadow got up, and the rest of his squad ran towards the hangar.

Soldiers sniped all of Shadow's squad but him.

The All-Father was there. "Hello...brother."

Shadow walked faster. "What do you mean?"

"You were the final project? You ever wonder what was between the Biolizard and you?"

Shadow stopped walking, and took a step back.

The All-Father took his hood off. He looked like Shadow, but colors reversed, with the eyes a bright red. "Shadow, you aren't the only Ultimate Life Form out there."

Shadow muttered "Impossible..."

The All-Father chuckled, "Nothing is impossible with the power of impurity. Join your relatives. Join...THE BROTHERHOOD OF SHADOWS!"

"W-who are you?" Shadow asked.

"Shadow-6. I was born with my Chaos Energy unusable. So, this amulet fixes, and focuses my negative chaos energy."

Shadow shook his head. "You killed good men!"

Shadow-6 glared and smirked. "They held you back! You need to know your real story! Your real friends! Us! Maria cared for all of us! We all have your pain!"

Shadow stared, envious. "You knew Maria?"

"We all did!" Shadow-6 replied. "And you know what? We can bring her back with you."

Shadow's eyes wavered. "F-fine. I'll join you."


	9. Chapter 9

Chapter Nine: Sonic's Charge

Sonic and Knuckles punched and kicked the Soldiers back, with Inferno and Tails running.

"Knuckles! I know how to put an end to this!" Sonic said.

"How?" Knuckles asked.

Sonic looked guilty. "I...I worked for them."

Knuckles's eyes shrunk. "W-what?"

"I know, I know, I'm a sinner! Now let's beat up my old bosses!"

Knuckles glared. "How do I know this isn't a trick?"

Sonic glared back. "Then why would I be punching my own guys?"

Knuckles nodded. "Fair enough."

They both ran to Tails.

"We're getting all the help we can and trashing the Brotherhood!" Sonic told Tails.

"Brotherhood?! Sonic...I don't even recognize you anymore..."

Just then, Ambush and Blackout arrived.

Sonic shouted to everyone, "Follow me!" as they ran to the Brotherhood's base.

Just then, Sonic was impaled by Vanix's blade.

Sonic slid off, barely alive.

Ambush, shocked, covered her mouth, then said, "Vanix! How could you?"

"It was the only way..." Vanix started to say. "The only way to save the Kingdom of Acorn. They would destroy everything Eggman's ever done! They would fix the legacy of my Kingdom which thy serves!"

Sonic, bleeding out of his stomach and mouth, said "You really t-think th-that's what t-they w-w-want?!"

Vanix glared, "You betrayed the All-Master! Even after he raised you, trained you!"

"And he would never care any more about me! I was a knight! I would never be his...his son."

Vanix's eyes widened. "Oh, sure. What a-" Vanix kicked him, and he rolled over. "-heartfelt story!"

Inferno couldn't even blink.

Tails was too scared to act.

Ambush, too worried that he'd kill him if she got close.

Knuckles, just plain terrified for his long-time friend.

Just then, the All-Master busted through the doors. "Vanix! What are you doing!"

Sonic perked his head up. "Hi, Dad. How's it hanging?"

The All-Master whipped his hood off. The similarities were staggering.

The quills were stationed exactly like one another.

The lack of chest hair.

The lack of fur on the arms and chest.

"Well, Daddy? You g-going t-to kill m-me like s-so so many others?"

Shadow-6 glared. "No. I'm going to reconnect your impurity. Make you mine once more...heheh. Shadow! Why don't you deal with the uninvited guests?"

Shadow walked out of the shadows, without his commander uniform.

Tails looked at Shadow, disgusted.

"No..." Sonic said.

Shadow smirked, then kicked Inferno. Ambush attempted to punch him, but, Shadow blocked and Chaos Speared her.

Shadow-6 held Sonic over his shoulder, and threw him onto the alter.

The drain was closed, and Sonic couldn't move.

They poured a black liquid into the altar.

"Someone has to save Sonic from his whacko dad!" Knuckles yelled.

Ambush got up. "I will!"

Shadow smirked. "Sure you will."

Shadow nearly homing attacked Ambush, but Knuckles uppercutted him away. By this time, it was dark, and a storm was brewing. Rain was beginning to fall.

Ambush sprinted towards the entrance, and followed the screams.

Sonic was yelping. The liquid was so saturated with malice, with hate, with evil, that it revived past failures, memories revitalized, like re-experiencing the worst moments of your life.

The All-Master chuckled, and the Black Emerald started to move.

It lifted upwards, and shot lightning.

Ambush attempted to break down the door to the altar room.

The All-Master noticed this, so he walked down and began his part of the ritual.

"O gods, Chaos, Gaia, and Solaris, please revitalize my Knight's connection to the 7 infinity's

impurity! To the Stars! To the dark! The negative! ILLUMINOS!"

Just then, Ambush busted through the doors, and ran to the altar, but it was too late. He absorbed and shot the lightning into the altar, reviving his connection to the impurity.

"NOOO!" She screamed.

The All-Master turned around and zapped her with lightning.

Sonic rose from the liquid, energized.

He was now pitch black, with no pupils and an angry yet slightly happy expression.

He was Dark Sonic. His incident.

He stepped out of the pool, and looked at Ambush. He reeled back to punch. Ambush got into a blocking position.

Then he hit Shadow-6, breaking his amulet, shattering 15 of his bones, and sending him flying.

Then his form faded away, and he fell into Ambush's arms. She barely caught him, but nonetheless she did.

She checked his pulse, and he was still alive.

She sat him down, and she sat down right next to him.

Meanwhile...

Shadow and Knuckles were fighting. Blow for blow, punch for punch, kick for kick, they were equal.

It was raining hard.

"That the best you can do?" Knuckles taunted.

"It was better than your- huh?" Shadow started as Shadow-6 was punched through the ceiling of the Brotherhood's base.

Dark Sonic stepped out.

"Well, at least you remember how to fight, Sonic."

Shadow-6 got up. "Your minor success has no meaning now. I can still use my power!"

Shadow-6's hands glowed dark purple. "You fight like a novice with this power!" He said as he punched Dark Sonic into the ground.

Dark Sonic's eyes widened and his aura glowed a bright red.

Dark Sonic blasted out dozens of chaos spears, all blocked, and Shadow-6 grabbed his throat.

"It's over, Sonic. I'm not just another villain. I'm your superior. Your weakness was inherited by your mother."

Dark Sonic blasted Shadow-6 backwards. He walked over to Shadow-6, who uppercutted him, and warped space around him, crushing his chest, Sonic was not able to breath.

He fell to the ground, and the super form dissipated.

"Goodbye, Sonic."

Sonic whispered, "Even now...you deny me...t-the title of son?"

Shadow-6 glared, smiling deviously. "You were never worthy of the title."

Sonic smiled.

"Why do you still smile, even on the verge of death?"

"B-because...Shadow-6...I'm not the one about to die."

Shadow stabbed Shadow-6 in the back with his dagger.

The ruby glowed brightly.

Shadow-6 turned around. "W-why...Brother?"

Shadow answered, "Shut up, Brother. I know where my allegiance lies."

Shadow-6 fell to his knees.

"Idiots! I kept this world together!"

Sonic replied, "Whatever happens because of this, we'll just stop. That's the one thing you never got, Dad. You can't have the world grow if you keep it in one place."

Shadow-6 clutched at his heart. "No! The 78 years...all of it..."

The rain poured harder.

"Lost..."

The rain lessened.

"...like tears..."

The rain lessened further.

"...in rain..."

Shadow-6 fell over, dead.

The rain ceased.

Finally, the sun peaked from the horizon.


	10. Epilogue

Epilogue: The Bright Future

Sonic sat at a hill, sunshine breaching the morning air.

It had been a few days since the end of the Brotherhood.

Shadow walked over. "You know, some Shadows are still alive."

"We'll catch them eventually. We always do."

Shadow scoffed, "Rats, scurrying to whatever hideouts they have left. Sonic, are you still connected? To the impurity?"

Sonic shook his head. "You can't get rid of a dark side. In some way or another, we all have our connections to the impurity. It's natural. To cut it off would be just as disastrous as cutting yourself off from the pure."

"Like your father did."

Sonic nodded, "Well, we better go catch those rats. See you later!"

And with that, Sonic ran off, to the sunrise...

...knowing full well that his previous adventure would not be his last.


End file.
